Code and data for "Bordetella adenylate cyclase toxin elicits chromatin remodeling and transcriptional reprogramming that blocks differentiation of monocytes into macrophages"

# Code and data for "Bordetella adenylate cyclase toxin elicits chromatin remodeling and transcriptional reprogramming that blocks differentiation of monocytes into macrophages"

- `pipeline` contains scripts for processing raw reads with `nf-core/rnaseq` Nextflow pipeline
  - `setup_conda.sh` sets up a conda environment for Nextflow
  - `samplesheet.csv` describes the samples
  - `rna-seq-nextflow.sh` runs the analysis
- `data` contains the quantifications by Salmon from the pipeline and data for the CRE motif (see `analysis.Rmd` for more details)
- `analysis.Rmd` an R notebook containing a code to reproduce conclusions and figures in the paper and additional comments.

The R environment (all packages) is reproducibly reconstructed via `renv` - run `renv::restore()` after loading the project.

The generated figures and tables are stored in the `outputs` directory.